Massarelli, E. et al. Combining immune checkpoint blockade and tumor-specific vaccine for patients with incurable human papillomavirus 16–related cancer. JAMA Oncol. 5, 67–73 (2019).

Article  PubMed  Google Scholar 

Weber, J. S. et al. Individualised neoantigen therapy mRNA-4157 (V940) plus pembrolizumab versus pembrolizumab monotherapy in resected melanoma (KEYNOTE-942): a randomised, phase 2b study. Lancet 403, 632–644 (2024).

Article  CAS  PubMed  Google Scholar 

Sette, A., Sidney, J. & Crotty, S. T cell responses to SARS-CoV-2. Annu. Rev. Immunol. 41, 343–73 (2023).

Article  CAS  PubMed  Google Scholar 

Bettencourt, P. et al. Identification of antigens presented by MHC for vaccines against tuberculosis. NPJ Vaccines 5, 2 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karunakaran, K. P. et al. Immunoproteomic discovery of novel T cell antigens from the obligate intracellular pathogen Chlamydia. J. Immunol. 180, 2459–2465 (2008).

Article  CAS  PubMed  Google Scholar 

Mayer, R. L. et al. Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes. Nat. Commun. 13, 6075 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stopfer, L. E. et al. MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas. Proc. Natl Acad. Sci. USA 119, e2208900119 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jaeger, A. M. et al. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature 607, 149–155 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hunt, D. F. et al. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255, 1261–1263 (1992).

Article  CAS  PubMed  Google Scholar 

Hunt, D. F. et al. Peptides presented to the immune system by the murine class II major histocompatibility complex molecule I-Ad. Science 256, 1817–1820 (1992).

Article  CAS  PubMed  Google Scholar 

Hunt, D. et al. In Methods in Protein Sequence Analysis (eds Imahori, K. & Sakiyama, F.) 127–133 (Springer, 1993).

Stopfer, L. E., Mesfin, J. M., Joughin, B. A., Lauffenburger, D. A. & White, F. M. Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition. Nat. Commun. 11, 2760 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chong, C., Coukos, G. & Bassani-Sternberg, M. Identification of tumor antigens with immunopeptidomics. Nat. Biotechnol. 40, 175–188 (2022).

Article  CAS  PubMed  Google Scholar 

Arieta, C. M. et al. The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection. Cell 186, 2392–2409.e21 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mohsen, M. O. et al. Bedside formulation of a personalized multi-neoantigen vaccine against mammary carcinoma. J. Immunother. Cancer 10, e002927 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Sellars, M. C., Wu, C. J. & Fritsch, E. F. Cancer vaccines: building a bridge over troubled waters. Cell 185, 2770–2788 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sahin, U. et al. Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer. Nature 547, 222–226 (2017).

Article  CAS  PubMed  Google Scholar 

Abelin, J. G. et al. Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction. Immunity 46, 315–326 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sarkizova, S. et al. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat. Biotechnol. 38, 199–209 (2020).

Article  CAS  PubMed  Google Scholar 

Abelin, J. G. et al. Defining HLA-II ligand processing and binding rules with mass spectrometry enhances cancer epitope prediction. Immunity 51, 766–779.e17 (2019).

Article  CAS  PubMed  Google Scholar 

Creech, A. L. et al. The role of mass spectrometry and proteogenomics in the advancement of HLA epitope prediction. Proteomics 18, e1700259 (2018).

Article  PubMed  Google Scholar 

Gallien, S., Kim, S. Y. & Domon, B. Large-scale targeted proteomics using internal standard triggered-parallel reaction monitoring (IS-PRM). Mol. Cell. Proteom. 14, 1630–1644 (2015).

Article  CAS  Google Scholar 

Hassan, C. et al. Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. J. Proteom. 109, 240–244 (2014).

Article  CAS  Google Scholar 

Stopfer, L. E. et al. Absolute quantification of tumor antigens using embedded MHC-I isotopologue calibrants. Proc. Natl Acad. Sci. USA 118, e2111173118 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rodenko, B. et al. Generation of peptide–MHC class I complexes through UV-mediated ligand exchange. Nat. Protoc. 1, 1120–1132 (2006).

Article  CAS  PubMed  Google Scholar 

Faridi, P., Purcell, A. W. & Croft, N. P. In immunopeptidomics we need a sniper instead of a shotgun. Proteomics 18, e1700464 (2018).

Article  PubMed  Google Scholar 

Li, K., Jain, A., Malovannaya, A., Wen, B. & Zhang, B. DeepRescore: leveraging deep learning to improve peptide identification in immunopeptidomics. Proteomics 20, e1900334 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Leddy, O., White, F. M. & Bryson, B. D. Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I. eLife 12, e84070 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lichti, C. F., Vigneron, N., Clauser, K. R., Van Den Eynde, B. J. & Bassani-Sternberg, M. Navigating critical challenges associated with immunopeptidomics-based detection of proteasomal spliced peptide candidates. Cancer Immunol. Res. 10, 275–284 (2022).

Article  CAS  PubMed  Google Scholar 

Kacen, A. et al. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nat. Biotechnol. 41, 239–251 (2023).

Article  CAS  PubMed  Google Scholar 

Prensner, J. R. et al. What can Ribo-Seq, immunopeptidomics, and proteomics tell us about the noncanonical proteome? Mol. Cell. Proteom. 22, 100631 (2023).

Article  CAS  Google Scholar 

Gessulat, S. et al. Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat. Methods 16, 509–518 (2019).

Article  CAS  PubMed